This sounds like it did not indeed install in the sandbox (compare the notice after "Resolving dependencies" in the hakyll install). Unfortunately I don't know what follows from here; it sounds like a cabal bug to me, but maybe being in the patched pandoc source directory keeps it from seeing the sandbox, in which case maybe there's an option to point to a specific sandbox for installs? (I still don't have a working Haskell install on my new machine, and am not sure at this point when I'll be able to get to it, sigh.)
--